Sixteen months after Haiti's devastating earthquake, many people are still living in tent cities In an interview with AP, Mr Rouzier said he hoped Bill Clinton would remain active in helping rebuild Haiti.
The agency was set up after the 2010 earthquake to assure foreign donors their funds would not be misspent.
Outgoing Haitian Prime Minister Jean-Max Bellerive is the other co-chair of the commission.
The countries that have contributed the most to rebuilding after the devastating earthquake, including the US, France and Japan, are also represented on the commission.
Bill Clinton has expressed his frustration at the slow pace of reconstruction in Haiti, but in January, one year after the earthquake, he said the speed of the effort was picking up.
A recent US government report criticised the commission for delays in its work.
'Tremendous vision' The 7.0-magnitude earthquake that struck Haiti on 12 January 2010 killed more than 250,000 people, made about two million people homeless and wrecked large parts of the capital, Port-au-Prince.
Mr Rouzier said a government agency would replace the "dysfunctional" commission Mr Rouzier was appointed prime minister by new President Michel Martelly and is awaiting senate confirmation of his role.
Mr Rouzier called the 27-member reconstruction commission "dysfunctional" and said it would be replaced by a government agency.
"What I can tell you is that the [commission] as it exists today will not continue," he told the Associated Press.
"I don't mean to crucify the people who came up with the concept. But sometimes when something doesn't work you have to fix it."
He said he would like Mr Clinton, who is also a UN envoy to Haiti, to remain active in the country's reconstruction.
"When you have someone of Clinton's calibre, this is a man of tremendous vision... We have to pick his brain and make sure that we have the right strategy."
Mr Rouzier is a US-educated businessman who runs several companies in Haiti, including a car dealership and an electric power company.
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